Mapping Quality Thresholds

The plot below shows the percentages of correctly and wrongly mapped reads for all mapping quality thresholds for this mapper. The values at threshold 0 therefore correspond to the unfiltered results.

Basic Statistics
Correctly Mapped21822891.102%
Wrongly Mapped212258.861%
Not Mapped890.037%
Total239542100.0%
Read Failure Statistics
Not mapped890.037%
Missing in mapper output00.0%
Mapped to wrong chromosome111974.674%
Mapped to wrong position100284.186%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.953400
Precision0.911400
Recall0.999600
Timing
Raw Mapping Time171.504s
Effective Mapping Time171.250s
Effective Init Time0.254s
Effective Time MeasureCPU
Mapping Time (Wall)43.778s
Mapping Time (CPU)171.504s
Mapping Time (CPU User)170.597s
Mapping Time (CPU System)0.907s
Init Time (Wall)0.274s
Init Time (CPU)0.254s
Init Time (CPU User)0.060s
Init Time (CPU System)0.194s
Additional Information
Mapper Memory Usage270 MB
Total Test Runtime (Wall)69.185s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory209960000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime0.19197
time0.276057004929
usrtime0.06299
working_directory/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory208676000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime0.19397
time0.27380490303
usrtime0.05999
working_directory/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory270640000
return0
status1
stderr
None
stdout
119771 reads; of these:
119771 (100.00%) were paired; of these:
110266 (92.06%) aligned concordantly 0 times
7117 (5.94%) aligned concordantly exactly 1 time
2388 (1.99%) aligned concordantly >1 times
----
110266 pairs aligned concordantly 0 times; of these:
91387 (82.88%) aligned discordantly 1 time
----
18879 pairs aligned 0 times concordantly or discordantly; of these:
37758 mates make up the pairs; of these:
89 (0.24%) aligned 0 times
1426 (3.78%) aligned exactly 1 time
36243 (95.99%) aligned >1 times
99.96% overall alignment rate
systime0.906862
time43.7781319618
usrtime170.597065
working_directory/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae